#ifndef READINPUTFILES_H
#define READINPUTFILES_H

#include<stdio.h>
#include <math.h>
#include<stdlib.h>
#include<time.h>
#include<string.h>
#include<ctype.h>
#include "common.h"
#include "fragmatrix.h"

int read_fragment_matrix(char* fragmentfile,struct fragment* Flist,int fragments );

// counts # of variants in VCF file, copies from rarevariantassociation testing code (readvcf.c), allows for arbitrary long lines
int count_variants_vcf(char* vcffile);

int read_vcffile(char* vcffile,struct SNPfrags* snpfrag,int snps);

int count_variants(char* variantfile);

int read_variantfile(char* variantfile,struct SNPfrags* snpfrag,int snps);

int read_haplotypefile(char* hapfile,struct SNPfrags* snpfrag,int snps,char* HAP1,char* initHAP,int* bn);

#endif
